"Tokyo Mew Mew" centers on Ichigo Momomiya, a high school girl who becomes infused with the DNA of an endangered species, the Iriomote wildcat, during a scientific experiment. This transformation grants her the abilities of a "Mew Mew," a warrior tasked with protecting Earth from alien parasites known as Chimera Animas. These creatures, created by an alien race called Deep Blue, seek to invade Earth by possessing animals and turning them into hostile monsters. Ichigo is joined by four other girls—Mint Aizawa, Retasu Midorikawa, Pudding Fong, and Zakuro Fujiwara—who are also infused with the DNA of endangered species, forming the Mew Mew team.

The series unfolds as Ichigo and her teammates balance their everyday lives with their responsibilities as Mew Mews. They must conceal their identities while battling Chimera Animas, which often appear in public spaces, threatening both humans and the environment. The team’s powers are tied to their animal DNA, granting them unique abilities such as enhanced agility, strength, and elemental attacks. Their battles are supported by a group of scientists led by Ryou Shirogane and Keiichiro Akasaka, who provide guidance and technological assistance.

A significant subplot involves Ichigo’s romantic relationship with Masaya Aoyama, a kind and popular classmate. However, her duties as a Mew Mew complicate their relationship, especially as she struggles to keep her secret identity hidden. The narrative also explores themes of environmental conservation, as the Mew Mews’ mission is intrinsically linked to protecting endangered species and the planet’s ecosystems.

As the story progresses, the Mew Mews confront increasingly powerful enemies, including the enigmatic leader of the alien invasion, Deep Blue. The team’s unity and determination are tested as they uncover the true motives behind the alien threat and the origins of their own powers. The series blends action, comedy, and romance, with a focus on teamwork, friendship, and the importance of preserving nature.